The events take place in a post-apocalyptic future, where Tokyo only exists as a simulated reality. The story follows Shogo Yahagi, a delinquent motorcyclist whose possession of a government prototype bike leads him to discover the truth about the city.
Shogo Yahagi lives in what appears to be 1980s metropolitan Japan. He meets Yui Takanaka and discovers her roommates are his friends Mai Yumekano and Tomomi Murashita. Shogo's old friend Shinji Nakagawa shows him a military prototype Garland motorcycle (labeled "Bahamut") that can reach over of 300km/h. He nearly escapes as Shinji is killed by unknown agents.
Shogo uses a public video phone to call Eve Tokimatsuri, a popular singer and TV host, during her show to expose the Garland to the public. The show's broadcast is cut off while Shogo shows Eve the bike (now painted red by a mechanic friend) and explains its capability. He escapes in another chase by agents and soon discovers it can also transform into a mecha.
Shogo helps Tomomi make an action film centered around the mysterious bike and has Yui hide the Garland at night. While looking for film locales, Shogo finds a secret entrance to a hidden, abandoned city and battles with some of the advanced fighters he encounters, most importantly with a military big shot named B.D.
After B.D. is nearly defeated, he informs Shogo about that Bahamut is a supercomputer that controls the events in this world, and that they are actually living on a spaceship, and that the real time is actually 500 years in the future. The military were developing new weapons underground to avoid Bahamut's detection, and that they have cleared "Level 6", Shogo shows mercy and leaves.
He then sneaks inside Eve's recording studio, and finds out that she is actually a computer simulated idol. In his anger at the state of the world, he nearly forces Yui to make love to him, but she supports and understands him anyway, and they have a romantic night. He confides in her everything he's learned about the world and watches martial law unfold on the city.
As the military clears "Level 7" of Eve's protection, B.D kills the Brass, manipulates the Prime Minister, and obtains financial support from the wealthy, notably Mai's father. Agents kill Tomomi and steal her master tapes, and a grief-stricken Mai returns to live with her father. Eve contacts Shogo through the Garland to ask him to help reactivate her reveals that the human race destroyed Earth, that there were actually 2 ships that left earth successfully and that Bahamut simulates the era of the 1980s because it was the most peaceful and full of love.
Shogo goes back to the underground city, and battles with the military, but is defeated by B.D., who returns Shogo's mercy by sending him back up to surface. Badly wounded, Shogo deserts the broken Garland and apparently walks back to Yui's place.
Shogo has been living underground for several months from the military and police. He teams up with the motorcycle gang "Trash" and reunites with Yui, who is part of the gang. While watching Eve's new music videos, Shogo sees her occasionally interrupt her video and ask for "Operator 7G", her codename for Shogo. In space, B.D.'s military has been fighting the alien race (the "Dezalg"), which uses an octopus-like penetrating weapon. As the fighting goes on, B.D. searches for Shogo, luring him into stealing another Garland. Shogo gets the Garland, escaping the trap, and uses it to contact Eve.
Trash has a showdown with the military in the city, where martial law is still in effect. In the battle, many of the members of Trash are wounded, including Yui. Lightning and Cindy help Shogo take Yui to Eve.
Shogo meets with Eve, who tries to heal Yui and reveals that Megazone is returning to Earth, but the planet has been protected by ADAM, which is programmed to destroy anything approaching the Earth except a select subset of the population chosen by ADAM. Eve admits ADAM is beyond her control, but she wishes Shogo the best and sends him off to reunite with Cindy and Lightning of Trash. B.D. arrives, apparently to challenge Shogo, but B.D. admits his helplessness in his position and also wishes Shogo good luck.
ADAM destroys the Dezalg ship and Megazone as what looks like an escape pod approaches the planet. Shogo deduces that the destruction will come soon, then sees Yui coming out of Eve's chamber. They start to step out of the building and see that they have landed on a peaceful Earth.
Part II is notable in abandoning the traditional anime style for more realistic looking characters. In addition, it contains more explicit scenes of violence and sex than its predecessor.
Part III is set hundreds of years after Part II and concerns a technologically advanced city on Earth, Eden, enclosed in a shield that ostensibly protects it from the outside but also keep humanity from repopulating the rest of the Earth until they are ready.
Eiji Takanaka is a hacker ("netjacker") and expert virtual gamer that hangs out in the virtual arcade, Psycholand. He starts working at E=X, the company, under the leadership of a mysterious Bishop Won Dai, that controls the shield and the city's information network, known as "The System." His friend Bud starts working at Orange, E=X's rival. Both friends play Orange's spacecraft simulator game called "Hard-On" (possibly a reference to the Sega game Hang-On), that is actively sent updates and new levels by the company. Orange seeks to complete a network independent of The System, and it uses its games to train fighters unconsciously for its cause.
Eiji goes out with Ryo Narahara, who works at the arcade; together they discuss life in Eden and the songs of Eve, whom Eden's population knows to be an artificial intelligence. She lures him to use his hacker skills to find her contact information. He finds her information deleted when using his terminal, so he and Bud try to find it by hacking the network in Eden's alleys.
At E=X, director Yacob Halm gives a speech about the importance of The System and decries netjackers. Operator Miura Simka privately warns Eiji about his activities, about which she has evidence, but she lets him go because of his invaluable skills. Yacob directs Eiji to use a Garland to catch netjackers. He takes it home to customize it.
Ryo visits Eiji, and they discuss Sion, an operator at Orange that has been challenging Eiji with new versions of the game in real time. His apartment heats up, and they escape through the window using the Garland, before it explodes. Sion hacks into the E=X network and finds a program called "Project Heaven." He and his Hargan units attack Eiji and their Garland units in a battle that Eiji predicted would happen between the two companies. Eiji and Sion end up joining forces as Sion explains that he was testing Eiji to see if he can awaken Eve. The company forces still battle. Eiji takes the Garland under the city and finds Eve's capsule. Eve awakens and addresses Eiji as "Operator 7G."
Eve takes Eiji outside Eden to the ruins of Megazone to check on Bahamut and explains its control of Megazone and guidance back to Earth. They see Eden's outside machinery stretching out further to maintain the city. Eve activates Bahamut to run diagnostics on Eden, which reports status as normal. Eve wonders why Shogo did not wake her and asks Bahamut what happened to him. Bahamut directs her to the last remaining file on him in the next room, which contains his Garland (from Part II) and a disk.
As Eve and Eiji return to Eden, Sion prepares to take over Orange from its leaders who only want to crush E=X. In the battle, Bud is brainwashed and fights for them but is killed in the process, despite Eiji's attempts to save him. They reach Bishop Won Dai, who they now know to be a Megazone survivor, to stop Project Heaven, which was planned to launch Eden into space to save Earth from humanity again. As the city starts to rumble in the execution of Project Heaven, Eiji shows Won Dai the disk, and he recognizes it and snaps out of his trance, realizing he has been connected to the system for too long. As he dies while Eiji attends to him, Eve takes the Bishop's place to stop Project Heaven. She kisses Eiji and "Shogo" goodbye through the glass shield that now surrounds her and brings the city back down, opening it back to nature. Eiji returns to the streets to find Ryo waiting for him and the fighting over.
The "International Edition" of Part II features an English-language voice cast and Japanese subtitles. It also includes footage from Robotech: The Movie -- the alternate ending mentioned above with voiced-over narration, used as an introduction to Part II. Here, Shogo is called "Johnny Winters," and Yui is called "Sue" (though her bike helmet still says Yui, as the video is the same). This Japan-only release version was originally on laserdisc, then in the out-of-print DVD Box Set. It is currently available as a Region 2 DVD bundled with the Limited Edition of the PS3 game Megazone 23: Aoi Garland.
Part III is only available on DVD in an 80 minute version in North America.
In 2007, ADV Films released a comprehensive 3-disc DVD entitled Megazone 23 Complete Collection. The first disc contains Megazone 23 (Part I). The second disc contains Megazone 23 Part II. The third disc contains Megazone 23 Part III: The Awakening of Eve and Day of Liberation. An audio option for English or Japanese with English subtitles is offered on each disc. Disc One includes a supplemental commentary for the first Megazone 23 movie featuring ADR directors Matt Greenfield, David Williams and Janice Williams.
In Part III, the Psycholand Video Arcade Employee database lists Yui, Tomomi, and Mai from Part I, as well as the surname Miyasato.